Change save path for localization analyses


I am using PYME Visualize to localize some SMLM data. I am wondering if I can change the location that it saves the analysis output. It currently defaults to the C-drive which is not where I keep my data.


Hi Lukas,

Is this the old style analysis (using the launchWorkers command) or new style (using PYMEClusterOfOne)? For the former, the environment variable PYMEDATADIR lets you specify the output directory. The latter will default to the value specified by the PYMEDATADIR environment variable, but this can also be over-ridden by the dataserver-root entry in the config files. On windows there are 2 config file locations - <your home directory>\.PYME\config.yaml for user config and <miniconda install directory>\etc\PYME\config.yaml which is used in a multi-user scenario (e.g. an instrument computer) to specify settings which apply to all users of the computer. The one under your home directory takes precedence, over-riding the settings for all users.

The config files are empty by default, so setting the PYMEDATADIR environment variable should work regardless of the analysis version as long as you haven’t added a dataserver-root entry to the config files. This might change in the future as we’re slowly moving away from using environment variables for config, but we will probably introduce a GUI editor for the config files before dropping environment variable support.


@DavidBaddeley just took a quick peek and we might need to shift things around to get the config doc page pulling from the in-file docstring. @lukasfue there are a couple other PYMEClusterOfOne options in the second link, though hopefully you should be set with the dataserver-root entry David mentioned. If you run into issues, make sure that your user owns the dataserver-root directory (see here)

Thanks for the quick responses @DavidBaddeley and @barentine. I’ll take a look at this when I get a chance.